The Matrix: Revisited
by Wetfish
Summary: Will Trinity and Neo's relationship stay strong when big things happen in The Real World?
1. The New Beginning

Disclaimer: I do not own the Matrix triolodgy or any of the characters from it.

This version of the Matrix is a carryon from Revolutions with a few changes. Neo and Trinity didn't die, Neo wasn't blinded by Bane, and Smith is back. His clones are no longer around, but Smith is still bad news- he's found a way to plug people from the matrix into the "real" world, and along with this new knowledge, he's teamed up with the machines and found himself a whole new army. This time, it really does look like the end…

It had certainly taken some getting used to. It was over 4 years since the truce between Zion and the machines had begun, and since then, all had been peaceful. Morpheus had even had a new version of The Nebuchadnezzar  
made, with updated technology, a new name (The N2), and a whole new crew. Well, not a whole new crew; Neo, Trinity and Morpheus were still aboard, but on Kid's eighteenth birthday he had been granted permission to join the ship, and three others had also been enlisted; Rain, Steel and Gunn. Kid had been in a good mood ever since getting granted the job.

Good mood until today.

It was around three hours off dawn when news reached the council, and since the fear caused was so big, it didn't take far to spread. An hour later, it was absolutely fact.

Smith was back.

"It's impossible," Trinity shook her head in disbelief as the N2's crew ate breakfast in near silence, broken only by these words.

Neo had a flash back to the day that he had fought Agent Smith in the Matrix and seen him die- or so he thought.

"Not impossible." Neo muttered. "Inevitable."

Trinity stared at Neo as he looked blankly into his breakfast bowl, as though waiting for something.

"What do you mean Neo?" she whispered as the rest of the crew talked amongst themselves.

Neo wasn't entirely sure how to answer. After a long pause he gave a little shrug and replied softly:

"Just something Smith said."

Trinity sighed and continued to eat her meal, not speaking to Neo again until Morpheus entered.

"Neo, what's wrong?" she asked, looking at Neo's blank expression and untouched food.

Morpheus spoke before Neo could say anything.

"I have received word from the council that Smith has formed an alliance with the machines." He spoke in a brave tone, with a slight hint of worry. "As you know, this could either mean peace or war for Zion."

I'm opting for the second. Neo thought, staring into his bowl, still full to the brim.

"Knowing Smith, he will try everything possible to turn the machines against us, but, with any luck, they will not come as easy as he hopes. If we can reach them before him, we may have a chance."

"But it's practically suicide, Sir!" Steel cried. He was the 19-year-old systems operator/hacker that had replaced Link early last year when he left to be with his new family.

Morpheus looked stern. "Then it's no different from most other days, is it?"

The crew fell deadly quiet.

"As I was saying," Morpheus continued. "If Neo and Trinity can reach Machine City, I think we are in with a chance." A few of the crewmembers nodded, but others didn't do anything.

At that moment, a messenger knocked on the ship's main door. Morpheus answered swiftly and the pair exchanged a few dark looks and brief words. After a few seconds, Morpheus returned and sighed.

"Apparently there's more." He looked around gravely before speaking once more. "Smith has found a way to plug people into our world, and they have the same privileges that we have in the matrix."

"What do you mean?" Steel asked, looking confused. "That they can use downloads too?"

"Exactly." Nodded Morpheus.

Many of the crew swore violently at this point.

"That's enough." Morpheus hushed them a minute later. "We have to attend a meeting immediately with the other ships' crews."

Everyone stood up and began to leave, but Neo didn't move. He was still staring at his breakfast as though waiting for something. Trinity lightly squeezed his shoulder and said smiling: "It's time to wake up, Alice." Before leaving to join the crew in the assembly room.

Neo sighed and slowly followed.


	2. In The Past

(Nearly 5 Years Previous)

Neo looked down at Bane's body, bloody and battered at his feet and he felt nothing more than sheer despair. His eyes still stung from the vicious attack that Bane had landed on him, but Neo was more concerned about Trinity. He stepped over the corpse and over to the ladder leading down to the lower deck, calling Trinity's name as he stepped further down. There was no reply except the echo of his voice rebounding off the walls.

Then, in the darkness, Neo very nearly fell over something. He crouched down, putting his hands along the floor, trying to figure out what or who was lying on the hard metal floor. With no means of light, and poor eyes to work with, Neo had to use his instinct- it was Trinity.

"Trin…"he whispered, putting a hand on what felt like her shoulder. "That bastard…what has he done to you?"

Neo knew he couldn't leave Trinity down here, but would he really be able to get her back up the ladder on his own? He spent two minutes making his decision before lifting her limp body up and stumbling towards the ladder. All in all, it took ten minutes to get Trin upstairs.

"Of course, you can't do much unconscious, can you?" Neo whispered to Trinity, smiling weakly, and looking around for somewhere to set her down. "Cabins." He said at last, spying an open door to his right. His vision was blurred, but not enough to stop him getting into the room and carefully putting the love of his life on the small, uncomfortable mattress. Neo knelt on the floor by Trinity, holding her hand for more than five minutes before bringing himself to get back to the pilot's seat.

Still with hazy sight, The One found his way back to the controls and began to start up again, piloting the ship further towards machine city.

"Sentinels!" Neo muttered, as two machines came hurtling towards him. "What would Trin do?" he asked himself. "What would Morpheus do?"

No time to decide- the damage was already taking place as the two machines began to attack the ship.

"Come on." Neo muttered. "You can do this Neo." And with this comment to himself, Neo pushed on the accelerator, trying to shake off the sentinels that were clinging to the ship, still trying to inflict damage.

A mighty crash and the sound of breaking glass as Neo flew the borrowed vessel straight into the side of the largest Sentinel that he had ever seen. It's octopus-like legs grabbed at Neo, but he dodged them, scrabbling out of his seat and running to the back of the ship.

"TRINITY!" he shouted as more Sentinels broke into the ship's armoured sides. "TRIN!"

Fast footsteps could be heard on the floor as Trinity flung the door of the cabin open and came face to face with Neo.

"Neo…what's happening…where's Bane…what happened to your eyes?" she looked confused, spinning around as though searching for an answer.

"No time." Neo shook his head, taking Trinity by the hand and pulling her to the nearest exit- a hole in the side of the ship about 4 meters away from the nearest ledge leading up to Machine City. "We have to jump."

"I can't do it Neo." Trinity said defiantly. "I can't do I-" Neo interrupted her.

"Trinity, if you don't, you and I will both die. I'm not doing this without you!" he said, urging her to just jump.

"But you're The One, Neo." Trinity argued. "Not me, not Morpheus, You, Neo."

"TRINITY, WE HAVEN'T GOT TIME!" Neo shouted. "JUST JUMP!"

"No, Neo." She shook her head. "I can't."

Neo looked into Trinity's eyes and felt her fear.

"You can't die, that's for sure." He muttered. "If you stay here, these Sentinels will rip you to shreds. Please jump, Trinity. Do it for me."

Tears formed in Trinity's grey-blue eyes, but she nodded and stepped back to take a run up. "Fine, Neo. I'll do it for you. But you have to promise me one thing."

"What?" Neo asked, trying to hurry her along.

The Sentinels were getting closer. This conversation was wasting precious time.

"That you'll kill that bastard Smith and his army of clones." She smiled a weak smile and ran towards the hole, jumping for her life.

"I promise…"Neo whispered as he watched her jump and reach the other side. "I promise. I promise." He repeated this, taking his own run-up and jumping, reaching the ledge on which Trinity was waiting for him. She grabbed him, and held him tight, never wanting to let go.

Just then, the ship on which they had arrived exploded, two or three Sentinels going with it. Trinity gasped, shocked at the impact, but Neo simply stared.

"We have to go. We have to find them." He said to Trin, taking her hand. "We have to climb this cliff."

The cliff was made from scrap metal, with sharp wires and corners everywhere.

"Then let's go." Trinity nodded, removing her hand from Neo's, and putting a shaky hand to the metal cliff, beginning on a voyage to the top.

Neo awoke much later. He didn't know how long he'd been gone, but he found himself in a strange room, white and clean looking. Trinity sat at his side, asleep. Important-seeming men and women were rushing around, talking and taking notes. They didn't seem to notice Neo had woken up.

"Excuse me?" Neo called to a woman just about to leave. "What's going on?"

The woman didn't seem to hear Neo and walked out of the room, scribbling something on her clipboard as she went.

Neo sighed, looking at the room with mild interest and confusion. It seemed like a hospital private room, with monitors and machine scattered and cabinets and cupboards around the place. The men and women had left now, leaving Trinity and Neo alone.

"Trin?" Neo whispering, tapping Trinity on the back with his hand. He noticed some kind of tubes had been attached to him. "Trinity?"

Trinity stirred slightly, sitting up and opening her eyes. When she saw Neo, she gave a tired smile.

"Good evening." She sighed, looking at him with pleased eyes.

"What?" Neo blinked. "What's happening?"

"You kept your promise." She grinned. "You killed Smith. The machines stopped attacking when you did it. But we thought you were dead. We didn't know you had survived. They brought you here about three months ago. Morpheus has just left to get something to eat."

"I…I…don't understand…" Neo said slowly. "What do you mean?"

Trinity sighed, knowing this was going to take along time.

"You and I went to Machine City, about five months ago. We went to negotiate with the machines. They sent you into the Matrix to find and defeat Smith, which you did. They brought you back here."

"But…where were you? Why didn't they bring you?"

Trinity looked at the ground for a minute or two, then to Neo again.

"I was unconscious." She smiled weakly. "I was out by the time you reached them. I woke up about two hours after you went in. They did bring me back, but I just don't remember it."

"How do you remember any of it if you were unconscious?" Neo frowned, still very confused. He was trying to take everything in at once.

"The machines told me what you were doing when I woke up. They said you'd gone to take care of something, and I should get some rest. So I did, and I woke up here four months ago. You arrived a month after I woke up. Don't ask me why- nobody had the guts to ask the machines why you'd been gone so long." Trinity finished her statement with a sigh. "Apparently, the machines told Morpheus you'd gone missing in the Matrix. They had to get someone to bring you back from there, and it wasn't easy."

"Why don't I remember?" Neo whispered. It was then he caught sight of himself in a mirror. His eyes, which he noticed looked fine from their state when Bane attacked them, no longer stung and he had perfect vision. "What happened to my eyes?"

Trinity smiled.

"I wondered when you'd ask that. The truth is, we're not 100 sure on that. When you arrived here they were as good as new, so maybe the machines did it. I don't know why they would though; they have a reputation as been selfish and I doubt they know how to address a grazed arm, let alone cure the blinded. Still, it's a good thing."

Whatever Neo was about to reply with, he never said it as the door was flung open and Morpheus, wearing a scruffy red jumper and black trousers, walked in, carrying two polystyrene cups and a bottle of water.

"He's awake." Morpheus nodded, his face full of reconciliation. "Good to have you back so soon, Neo."

"What?" Neo asked, a little surprised at Morpheus. "Soon? I've been out cold for months!"

"Which could have easily been years." Morpheus replied cryptically, sitting on a chair placed next to Trinity's. He handed her a cup and the bottle of water.

Trinity poured the water into the cup and handed it to Neo.

"Sit up. You need something to drink." She commanded.

Neo propped himself up a little, sipping from the cup. "Who were the men and women in here earlier?" he asked after taking a gulp of water.

"Doctors, researchers, nurses- just about the whole Zion Medical team." Morpheus shrugged. "They've been watching your progress since you came back, Neo. It was doubtful you'd make it. Some wanted to give you one more week before the turned the machines off."

"But I wouldn't have let them anyway." Trinity scowled. "They don't believe in anything anymore. They close their eyes and shut their ears to the unlikely."

"Realists." A new voice was heard, as a female walked in, carrying a clipboard. "There's not point in searching for something that isn't there."

"Jet, you were wrong. Accept it." Trinity said coolly. "He's sat up, drinking water and talking to me. You would have killed a healthy man had you turned that machine off last week." She gestured to a large black box in the corner of the room.

"I'm the doctor around here, not you." Jet snapped. "And I'll be the one saying who lives and who dies. He was costing us too much money to keep alive. What else were we meant to do?"

"It's always about money, Jet." Trinity said angrily. "Forget about human morals- it's the money that matters."

"It is when money is what's keeping us alive!" Jet hissed furiously. "And I advise you not to say things live that in the future, especially in front of Fort."

With these heated words, Jet stormed out of the room again.

"Who's Fort?" Neo asked curiously, after a long pause.

There was another minute of silence before Morpheus spoke.

"Fort is the head of medicine, and a member of the elder's council. He's also Jet's father, and very traditional, but a nice man inside. Fort is the one that gave permission for your life machines to be kept on."

"Although Jet still thinks he's on her side. What a pompous girl she is." Trinity chuckled. "I do feel sorry for Steel."

"Who's Steel?" Neo asked, still feeling like there was something he was missing.

"Steel is Jet's son. He's joining the crew to replace Link." Morpheus replied as Trinity was drinking from the water bottle.

"Why; where's Link?" Neo enquired, feeling he was beginning to ask too many questions.

"Link decided he wanted to stay on Zion to help his wife raise their new son." Morpheus smiled slightly. "And we've got more new crew than just Steel. We enlisted two newbies- Rain and Gunn and…" he was interrupted by Trinity.

"KID!" she shouted crossly. "He let Kid join us!"

Neo gasped, as Morpheus glowered at Trinity. Then, Neo burst out laughing.

"Good joke!" he smiled. "Nearly had me there."

No body else was laughing.

"Oh." He said quietly, smile fading from his face.

"I'll introduce you to the rest of the crew later." Morpheus spoke after more silence. "But for now, rest. We need to get you out and on the ship tomorrow."


	3. A Shock for Zion

"ZION! HERE ME!" the roar of the voice belonging to Captain Morpheus echoed through the assembly hall, as it had done so many times before. The murky colours below his mighty podium were the inks of the Zion inhabitants, in bleak clothes and bland expression. Parents held their young ones tight- and those with none feared for themselves. The N2's crew exchanged awkward glances from their own seats and Trinity held Neo's hand from the seat next to him.

"I'll be frank-" Morpheus continued. "Agent Smith is back and he's bigger and better than before." He waited for a shocked murmur amongst the crowds but there was none. This was old news.

Commander Lock stepped up behind Morpheus and proclaimed loudly: "There is no need to panic. We are dealing with this."

"We're past panic!" Neo spoke for the first time, standing up and pushing his way to the podium. Then there was murmur from below. "Commander Lock thinks we've got everything under control, but he knows it himself. Smith's getting the machines again and we don't really stand a chance."

Someone shouted a comment about Neo's alignment as "The One." He gave a sad laugh and shook his head. "The One can't save you now. Go one- here's my advice to Zion- run. Don't stick around and try to wait it out. Take your children, take your wives and go." Morpheus rolled his eyes and Lock tried to fight Neo for the centre stage, but Neo stood firm. "If you thought the first one was bad, then you'll think this one's the apocalypse now. But you don't believe in God, do you? Because right now, there's no point. No higher being can stop him now."

The many Zion residents were silenced as Neo sighed an angry sigh. "Don't try and be fooled again." He left the stand and stormed back to his cabin. Lock turned to Trinity and glared at her, as though she had somehow influenced him. She looked through grey eyes to her black shoes and tugged at a loose thread on her jumper. Morpheus muttered to himself and exited the hall, as many of the hoards were doing. Commander Lock shouted profanities and left gesturing about Neo's "absurd" performance.

_Absurd, but true and to the point. _Trinity thought as she led the N2's remaining crew back to the ship.

"Neo?" Trinity whispered comfortingly as she slipped through the metal door to his bedroom. There he was- lied on the bed, facing the wall and looking most uncomfortable. Trinity gave a sad sigh and sat on the bed, stroking his head. "Why did you do that today? Morpheus didn't want anyone to panic. He knew that was what should be said, but he couldn't do it."

"Well, I could." Neo replied hotly, not budging. He could be so stubborn sometimes- it upset Trinity to see him like this, and she hated his bad moods.

"Neo, we can't worry them too much." Trinity sighed again, looking at him with desperation. "We know it's coming, but we can't let them know. Zion will break without them, and we can't keep them under control and hold off Smith at the same time, can we?"

Neo didn't respond to this, but he didn't have time anyway as Morpheus entered the cabin.

"I can go if you want to speak to Neo." Trinity stood up, about to exit.

"No Trinity- I need to speak to you both." Morpheus sat down in a nearby chair and a little surprised, Trinity sat down on the bed again. Neo still refused to shift.

Morpheus wore a stern look, but there was a trace of worry and urgency in his face. "The Council of Elders want someone to go into the Matrix to do some undercover work. It's something we haven't tried before, but we think it's worth a shot. They use it in the Matrix and it's quite successful."

"Let me guess." Neo interrupted. "They want me to go?"

"No, actually." Morpheus shook his head. He had expected this reaction. "The council want Trinity to go."


End file.
